pycode-kg 0.18.2__tar.gz → 0.19.1__tar.gz

pycode_kg-0.19.1/PKG-INFO

@@ -0,0 +1,308 @@
+Metadata-Version: 2.4
+Name: pycode-kg
+Version: 0.19.1
+Summary: A tool to build a searchable knowledge graph from Python repositories
+License-Expression: Elastic-2.0
+License-File: LICENSE
+Keywords: knowledge-graph,code-analysis,ast,lancedb,sqlite,semantic-search
+Author: Eric G. Suchanek, PhD
+Author-email: suchanek@mac.com
+Requires-Python: >=3.12,<3.14
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Provides-Extra: all
+Provides-Extra: dev
+Provides-Extra: kgdeps
+Provides-Extra: viz
+Provides-Extra: viz3d
+Requires-Dist: PyQt5 (>=5.15.0) ; extra == "all"
+Requires-Dist: PyQt5 (>=5.15.0) ; extra == "viz3d"
+Requires-Dist: click (>=8.1.0,<9)
+Requires-Dist: detect-secrets (>=1.5.0) ; extra == "all"
+Requires-Dist: detect-secrets (>=1.5.0) ; extra == "dev"
+Requires-Dist: doc-kg (>=0.11.0) ; extra == "dev"
+Requires-Dist: doc-kg (>=0.11.0) ; extra == "kgdeps"
+Requires-Dist: kgmodule-utils (>=0.2.1)
+Requires-Dist: lancedb (>=0.29.0)
+Requires-Dist: markdown (>=3.6) ; extra == "all"
+Requires-Dist: markdown (>=3.6) ; extra == "viz3d"
+Requires-Dist: mcp (>=1.0.0)
+Requires-Dist: mypy (>=1.10.0) ; extra == "all"
+Requires-Dist: mypy (>=1.10.0) ; extra == "dev"
+Requires-Dist: numpy (>=1.24.0)
+Requires-Dist: pandas (>=2.0.0)
+Requires-Dist: param (>=2.0.0) ; extra == "all"
+Requires-Dist: param (>=2.0.0) ; extra == "viz3d"
+Requires-Dist: pdoc (>=14.0.0) ; extra == "all"
+Requires-Dist: pdoc (>=14.0.0) ; extra == "dev"
+Requires-Dist: plotly (>=5.14.0) ; extra == "all"
+Requires-Dist: plotly (>=5.14.0) ; extra == "viz"
+Requires-Dist: pre-commit (>=4.5.1) ; extra == "all"
+Requires-Dist: pre-commit (>=4.5.1) ; extra == "dev"
+Requires-Dist: pylint (>=4.0.5) ; extra == "all"
+Requires-Dist: pylint (>=4.0.5) ; extra == "dev"
+Requires-Dist: pytest (>=8.0.0) ; extra == "all"
+Requires-Dist: pytest (>=8.0.0) ; extra == "dev"
+Requires-Dist: pytest-cov (>=5.0.0) ; extra == "all"
+Requires-Dist: pytest-cov (>=5.0.0) ; extra == "dev"
+Requires-Dist: pyvis (>=0.3.2) ; extra == "all"
+Requires-Dist: pyvis (>=0.3.2) ; extra == "viz"
+Requires-Dist: pyvista[jupyter] (>=0.44.0) ; extra == "all"
+Requires-Dist: pyvista[jupyter] (>=0.44.0) ; extra == "viz3d"
+Requires-Dist: pyvistaqt (>=0.11.0) ; extra == "all"
+Requires-Dist: pyvistaqt (>=0.11.0) ; extra == "viz3d"
+Requires-Dist: rich (>=14.3.3,<15)
+Requires-Dist: ruff (>=0.4.0) ; extra == "all"
+Requires-Dist: ruff (>=0.4.0) ; extra == "dev"
+Requires-Dist: safetensors (>=0.5.0)
+Requires-Dist: sentence-transformers (>=5.4.1)
+Requires-Dist: streamlit (>=1.35.0) ; extra == "all"
+Requires-Dist: streamlit (>=1.35.0) ; extra == "viz"
+Requires-Dist: torch (>=2.5.1)
+Requires-Dist: trame-vtk (>=2.0.0) ; extra == "all"
+Requires-Dist: trame-vtk (>=2.0.0) ; extra == "viz3d"
+Requires-Dist: transformers (>=4.40.0,<4.57)
+Project-URL: Homepage, https://github.com/Flux-Frontiers/pycode_kg
+Project-URL: Repository, https://github.com/Flux-Frontiers/pycode_kg
+Description-Content-Type: text/markdown
+
+
+<p align="center">
+  <img src="assets/logos/pycodeKG.PNG" alt="PyCodeKG" width="200"/>
+</p>
+
+[![Python](https://img.shields.io/badge/python-3.12%20%7C%203.13-blue.svg)](https://www.python.org/)
+[![License: Elastic-2.0](https://img.shields.io/badge/License-Elastic%202.0-blue.svg)](https://www.elastic.co/licensing/elastic-license)
+[![Version](https://img.shields.io/badge/version-0.19.1-blue.svg)](https://github.com/Flux-Frontiers/pycode_kg/releases)
+[![CI](https://github.com/Flux-Frontiers/pycode_kg/actions/workflows/ci.yml/badge.svg)](https://github.com/Flux-Frontiers/pycode_kg/actions/workflows/ci.yml)
+[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
+[![DOI](https://zenodo.org/badge/1202379010.svg)](https://zenodo.org/badge/latestdoi/1202379010)
+
+# PyCodeKG — A Knowledge Graph for Python Codebases
+
+**PyCodeKG turns a Python codebase into a deterministic, queryable knowledge graph — and uses it to produce architectural analyses you can act on, with or without an LLM in the loop.**
+
+It walks the AST of every module, class, function, and method in your repo, extracts the typed relationships that actually hold the code together (`CONTAINS`, `CALLS`, `IMPORTS`, `INHERITS`, `RESOLVES_TO`), and stores the result in SQLite. A LanceDB vector index sits alongside the graph so that *"authentication flow"* and *"verify_jwt"* both find the right place to start exploring. From there you can rank functions by structural importance, trace fan-in across import aliases, detect circular imports and dead code, render the call graph in 3D, snapshot metrics for diffing across releases, or hand the whole thing to Claude over MCP.
+
+The original motivation was simple: **produce thorough, defensible analyses of Python codebases that don't depend on inference**. Every result is computed from the AST and the graph — no model is asked to guess. When an LLM is present, it consumes the *same* grounded output as a structured context pack, and the hallucinations that plague "embed-the-repo" tools largely disappear.
+
+Everything runs on your laptop. No cloud APIs, no quotas, no source code leaving the machine.
+
+[Technical Paper (PDF)](article/pycode_kg.pdf) · *Author: Eric G. Suchanek, PhD — Flux-Frontiers, Liberty TWP, OH*
+
+---
+
+## Sister projects
+
+PyCodeKG is part of a growing family of knowledge-graph systems that share the same hybrid semantic-plus-structural design — each one applies it to a different kind of corpus:
+
+- **[DocKG](https://github.com/Flux-Frontiers/doc_kg)** — Markdown and prose. Indexes PyCodeKG's own documentation, so the docs you're reading are themselves a queryable graph.
+- **[MetaboKG](https://github.com/Flux-Frontiers/metabo_kg)** — metabolic pathway data (KEGG, SBML, BioPAX), with FBA / ODE simulation on top of the graph.
+- **[DiaryKG](https://github.com/Flux-Frontiers/diary_kg)** — personal journals and diary corpora; semantic search and graph traversal over a writer's body of work.
+- **[FTreeKG](https://github.com/Flux-Frontiers/FTreeKG)** — filesystem trees as a queryable graph of directories, files, and contents.
+- **[AgentKG](https://github.com/Flux-Frontiers/agent_kg)** — conversational memory as a knowledge graph: turns, decisions, commitments, preferences, and the relationships between them.
+
+Together they form **KGRAG**, a federated retrieval layer where one query can span code, documentation, journals, filesystems, agent memory, and domain data simultaneously.
+
+---
+
+## Two ways to use it
+
+PyCodeKG is designed to be useful at both ends — as a standalone command-line analysis tool, and as a structured context layer for AI agents.
+
+### 1. Standalone — `pycodekg analyze`
+
+This single command is the actual reason I wrote this module. I got tired of my LLM doing grep on my src/ in order to get a good analysis of the codebase. This command runs fifteen analysis passes in seconds and the output drops straight into your favorite coding LLM for targeted improvement suggestions. I used this process to iteratively improve PyCodeKG and several of the analysis passes were added as a result.
+
+The analysis/ has files *_analysis_<date>.md - I ran PyCodeKG against **numpy** and **matplotlib** for fun.
+
+```bash
+pycodekg init                                        # downloads embedder
+pycodekg build --repo .                              # one-time index
+pycodekg analyze.                                    # the full report
+```
+
+**Note**
+The first-time run can take some time to warm up. Be patient.
+
+The 15-phase pipeline runs in sequence and surfaces several important metrics:
+
+| # | Phase | What it surfaces |
+|---|-------|-----------------|
+| 1 | Baseline metrics | Node/edge counts, graph shape |
+| 2 | CodeRank (global PageRank) | Structurally most important symbols |
+| 3 | Fan-in analysis | Heavily depended-on functions (breaking-change risk) |
+| 4 | Fan-out analysis | Orchestrators and complexity hotspots |
+| 5 | Dependency analysis | Orphaned / dead code candidates |
+| 6 | Pattern detection | Anti-patterns and structural red flags |
+| 7 | Module coupling | Tightly coupled pairs, import graph density |
+| 8 | Critical paths | Longest call chains, bottlenecks |
+| 9 | Public API identification | Exposed vs. internal surface |
+| 10 | Docstring coverage | By module, class, function, method |
+| 11 | Inheritance hierarchy | Depth, multiple inheritance, diamond patterns |
+| 12 | Insight synthesis | Issues + strengths callouts |
+| 13 | Snapshot history | Metric trends across releases |
+| 14 | Structural centrality (SIR) | Bridge nodes, graph removal impact |
+| 15 | Concern-based ranking | Nodes grouped by architectural concern |
+
+Every finding maps to a file and line number — no hallucinated signatures, no probabilistic guesses. The Markdown output is LLM-ready; the JSON snapshot is CI-gate-ready. Reach for `analyze` before any non-trivial refactor, at every release, and whenever you inherit an unfamiliar codebase. Full reference: [docs/Analyze.md](docs/Analyze.md).
+
+```bash
+pycodekg analyze --quiet --json ~/.claude/pycodekg_analysis_latest.json
+jq '.docstring_coverage.total' ~/.claude/pycodekg_analysis_latest.json
+```
+
+### 2. Agentic — MCP server for grounded AI workflows
+
+Run `pycodekg mcp` and Claude (or any MCP-aware client) gets nineteen tools backed by the same graph: `graph_stats`, `query_codebase`, `pack_snippets`, `get_node`, `list_nodes`, `callers`, `explain`, `centrality`, `bridge_centrality`, `framework_nodes`, `analyze_repo`, `snapshot_list / show / diff`, and more. Setup for Claude Code, Claude Desktop, Kilo Code, Copilot, and Cline is a single line — see [docs/MCP.md](docs/MCP.md) and [docs/INSTALLATION.md](docs/INSTALLATION.md).
+
+The agent benefit isn't subtle. Tools like `pack_snippets` return *actual source* with line numbers and surrounding context; `callers` returns the *real* fan-in resolved across import aliases, not a regex's best guess. The agent stops fabricating function signatures and starts citing them. Multi-step workflows — *"find the auth path, list its callers, summarize what changes if I rename it"* — collapse from dozens of `grep`s and file reads into a handful of source-grounded calls.
+
+Independent assessments tend to put it the same way:
+
+> "PyCodeKG compresses a multi-step workflow — semantic search, graph expansion, caller tracing, snippet retrieval, and architectural summarization — into a small set of tools that are fast to invoke and easy to chain. In practice, it let me move from broad orientation to intent-driven discovery and then to structural validation without dropping down into manual grep or repeated file reads."
+> — *GPT-5 (via Cline)*
+
+> "What sets it apart from 'search the repo with embeddings' tools is the structural layer… Verdict: 4.5/5 — recommend without reservation for any non-trivial Python codebase."
+> — *Claude Opus 4.7*
+
+> "PyCodeKG is dramatically more effective than traditional grep/file-reading workflows. Unique value: hybrid search combining natural-language intent with precise structural relationships."
+> — *Claude Haiku 4.5*
+
+Full reports in [assessments/](assessments/).
+
+---
+
+## Get started in 60 seconds
+
+**Requirements:** Python ≥ 3.12, < 3.14
+
+```bash
+pip install 'pycode-kg[viz,viz3d]'        # base + Streamlit + 3-D viewer
+
+cd /path/to/your/repo
+pycodekg init --repo .                    # download model, build graph, install hooks, snapshot
+pycodekg analyze .                        # the architectural report
+```
+
+That's the recommended path. Variants (minimal install, MCP-only, contributor setup) are in [docs/INSTALLATION.md](docs/INSTALLATION.md). Every CLI subcommand is also exposed as a script alias (`pycodekg-analyze`, `pycodekg-build`, `pycodekg-mcp`, …) for use in Makefiles and Poetry projects.
+
+---
+
+## How retrieval works
+
+Search is hybrid by design. A query like *"authentication flow"* runs in two phases:
+
+1. **Vector phase** — the query is embedded with a local sentence-transformer (cached after first download) and LanceDB returns the `k` closest functions, classes, and modules by cosine similarity.
+2. **Graph expansion phase** — each seed hit is expanded `hop` BFS steps along the typed edges (`CONTAINS`, `CALLS`, `IMPORTS`, `INHERITS`, `RESOLVES_TO`) so call chains and module relationships surface alongside the names that matched.
+
+**Structure is treated as ground truth; the embeddings are strictly an acceleration layer.** When the graph and the vector index disagree, the graph wins. This is why fan-in lookups are accurate even for same-named symbols across modules — `RESOLVES_TO` edges bridge call sites through their import aliases, and `callers()` does a two-phase reverse traversal that grep simply cannot replicate.
+
+The graph is built around four node kinds (module, class, function, method) and five edge relations. Schema and edge semantics are documented in [docs/CHEATSHEET.md](docs/CHEATSHEET.md).
+
+---
+
+## What you can do with it
+
+| If you want to… | Reach for | Detail |
+|---|---|---|
+| **Get a thorough architectural report** | `pycodekg analyze` | [docs/Analyze.md](docs/Analyze.md) |
+| **Generate a coherent architecture description** | `pycodekg architecture` | [docs/Architecture_usage.md](docs/Architecture_usage.md) |
+| **Track metrics across releases** | `pycodekg snapshot save / list / diff` | [docs/SNAPSHOTS.md](docs/SNAPSHOTS.md) |
+| **Identify the most structurally important code** | `pycodekg centrality` (SIR PageRank) | [docs/CODERANK.md](docs/CODERANK.md) |
+| **Pull source-grounded context for an LLM** | `pycodekg pack "..." --format md` | [docs/CHEATSHEET.md](docs/CHEATSHEET.md) |
+| **Run a hybrid semantic + structural query** | `pycodekg query "..."` | [docs/CHEATSHEET.md](docs/CHEATSHEET.md) |
+| **Browse the graph interactively** | `pycodekg viz` (Streamlit) | [docs/INSTALLATION.md](docs/INSTALLATION.md) |
+| **See call graphs in 3-D** *(active development — functional but rough)* | `pycodekg viz3d --layout funnel` | [docs/VIZ3D.md](docs/VIZ3D.md) |
+| **Wire it into Claude / Copilot / Cline** | `pycodekg mcp` | [docs/MCP.md](docs/MCP.md) |
+
+If you only read one doc after this one, read [docs/Analyze.md](docs/Analyze.md) — that's where most of the day-to-day value lives.
+
+---
+
+## Architecture
+
+```
+src/pycode_kg/
+├── visitor.py                       # AST extraction (three-pass: structure, calls, dataflow)
+├── graph.py                         # GraphBuilder: file discovery + dispatch
+├── store.py                         # SQLite persistence + canonical edges
+├── index.py                         # LanceDB semantic index
+├── pycodekg.py                      # Public façade
+├── pycodekg_query.py                # Hybrid query
+├── pycodekg_snippet_packer.py       # Source-grounded packs
+├── pycodekg_thorough_analysis.py    # `analyze` engine
+├── architecture.py                  # `architecture` description generator
+├── ranking/                         # PageRank, bridge centrality, framework nodes
+├── snapshots.py                     # Temporal metric snapshots
+├── analysis/                        # Coupling, cycles, orphans, hotspots
+├── cli/                             # All `pycodekg-*` entry points
+├── mcp_server.py                    # MCP server (nineteen tools)
+├── app.py                           # Streamlit web app
+├── viz3d.py / layout3d.py           # PyVista/PyQt5 3-D viewer
+└── viz3d_timeline.py                # Metric history timeline
+```
+
+The MCP server, the CLI, and the Streamlit app are thin wrappers over the same store + index + ranking core — there is exactly one code path for each capability. The latest architectural deep-dive is in [docs/analysis_v0.19.0.md](docs/analysis_v0.19.0.md), produced (of course) by `pycodekg analyze` against this very repo.
+
+---
+
+## Documentation map
+
+| Doc | What it covers |
+|---|---|
+| [docs/INSTALLATION.md](docs/INSTALLATION.md) | All install variants, MCP setup, contributor setup, troubleshooting |
+| [docs/Analyze.md](docs/Analyze.md) | The `analyze` command — every metric, every flag, interpretation guide |
+| [docs/Architecture_usage.md](docs/Architecture_usage.md) | Generating coherent architecture descriptions |
+| [docs/SNAPSHOTS.md](docs/SNAPSHOTS.md) | Temporal metric snapshots, diffing across releases |
+| [docs/CODERANK.md](docs/CODERANK.md) | SIR PageRank, bridge centrality, framework hubs |
+| [docs/MCP.md](docs/MCP.md) | MCP server setup for Claude / Kilo / Copilot / Cline, tool reference |
+| [docs/CHEATSHEET.md](docs/CHEATSHEET.md) | Every CLI flag and every MCP tool — one page |
+| [docs/VIZ3D.md](docs/VIZ3D.md) | The 3-D PyVista viewer and layouts |
+| [CHANGELOG.md](CHANGELOG.md) | Release history |
+
+---
+
+## Citation
+
+If you use PyCodeKG in your research or project, please cite it:
+
+[![DOI](https://zenodo.org/badge/1202379010.svg)](https://zenodo.org/badge/latestdoi/1202379010)
+
+> Suchanek, E. G. (2026). *PyCodeKG: A Knowledge Graph for Python Codebases* (Version 0.19.0) [Software]. Flux-Frontiers. https://doi.org/10.5281/zenodo.19834777
+
+```bibtex
+@software{suchanek_pycode_kg,
+  author    = {Suchanek, Eric G.},
+  title     = {{PyCodeKG}: A Knowledge Graph for Python Codebases},
+  version   = {0.19.0},
+  year      = {2026},
+  publisher = {Flux-Frontiers},
+  url       = {https://github.com/Flux-Frontiers/pycode_kg},
+  doi       = {10.5281/zenodo.19834777},
+}
+```
+
+---
+
+## License
+
+[Elastic License 2.0](https://www.elastic.co/licensing/elastic-license) — free for non-commercial and internal use; commercial redistribution or hosting requires a license from Flux-Frontiers.
+
+---
+
+## Support & acknowledgments
+
+- **Issues** — [GitHub Issues](https://github.com/Flux-Frontiers/pycode_kg/issues)
+- Sister projects [DocKG](https://github.com/Flux-Frontiers/doc_kg) and [MetaboKG](https://github.com/Flux-Frontiers/metabo_kg)
+- LanceDB, sentence-transformers, PyVista, Streamlit, and FastMCP for the foundations
+
+---
+
+*Built for Python developers and AI agents that work alongside them — egs · Last updated May 2026*
+

pycode_kg-0.19.1/README.md

@@ -0,0 +1,234 @@
+
+<p align="center">
+  <img src="assets/logos/pycodeKG.PNG" alt="PyCodeKG" width="200"/>
+</p>
+
+[![Python](https://img.shields.io/badge/python-3.12%20%7C%203.13-blue.svg)](https://www.python.org/)
+[![License: Elastic-2.0](https://img.shields.io/badge/License-Elastic%202.0-blue.svg)](https://www.elastic.co/licensing/elastic-license)
+[![Version](https://img.shields.io/badge/version-0.19.1-blue.svg)](https://github.com/Flux-Frontiers/pycode_kg/releases)
+[![CI](https://github.com/Flux-Frontiers/pycode_kg/actions/workflows/ci.yml/badge.svg)](https://github.com/Flux-Frontiers/pycode_kg/actions/workflows/ci.yml)
+[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
+[![DOI](https://zenodo.org/badge/1202379010.svg)](https://zenodo.org/badge/latestdoi/1202379010)
+
+# PyCodeKG — A Knowledge Graph for Python Codebases
+
+**PyCodeKG turns a Python codebase into a deterministic, queryable knowledge graph — and uses it to produce architectural analyses you can act on, with or without an LLM in the loop.**
+
+It walks the AST of every module, class, function, and method in your repo, extracts the typed relationships that actually hold the code together (`CONTAINS`, `CALLS`, `IMPORTS`, `INHERITS`, `RESOLVES_TO`), and stores the result in SQLite. A LanceDB vector index sits alongside the graph so that *"authentication flow"* and *"verify_jwt"* both find the right place to start exploring. From there you can rank functions by structural importance, trace fan-in across import aliases, detect circular imports and dead code, render the call graph in 3D, snapshot metrics for diffing across releases, or hand the whole thing to Claude over MCP.
+
+The original motivation was simple: **produce thorough, defensible analyses of Python codebases that don't depend on inference**. Every result is computed from the AST and the graph — no model is asked to guess. When an LLM is present, it consumes the *same* grounded output as a structured context pack, and the hallucinations that plague "embed-the-repo" tools largely disappear.
+
+Everything runs on your laptop. No cloud APIs, no quotas, no source code leaving the machine.
+
+[Technical Paper (PDF)](article/pycode_kg.pdf) · *Author: Eric G. Suchanek, PhD — Flux-Frontiers, Liberty TWP, OH*
+
+---
+
+## Sister projects
+
+PyCodeKG is part of a growing family of knowledge-graph systems that share the same hybrid semantic-plus-structural design — each one applies it to a different kind of corpus:
+
+- **[DocKG](https://github.com/Flux-Frontiers/doc_kg)** — Markdown and prose. Indexes PyCodeKG's own documentation, so the docs you're reading are themselves a queryable graph.
+- **[MetaboKG](https://github.com/Flux-Frontiers/metabo_kg)** — metabolic pathway data (KEGG, SBML, BioPAX), with FBA / ODE simulation on top of the graph.
+- **[DiaryKG](https://github.com/Flux-Frontiers/diary_kg)** — personal journals and diary corpora; semantic search and graph traversal over a writer's body of work.
+- **[FTreeKG](https://github.com/Flux-Frontiers/FTreeKG)** — filesystem trees as a queryable graph of directories, files, and contents.
+- **[AgentKG](https://github.com/Flux-Frontiers/agent_kg)** — conversational memory as a knowledge graph: turns, decisions, commitments, preferences, and the relationships between them.
+
+Together they form **KGRAG**, a federated retrieval layer where one query can span code, documentation, journals, filesystems, agent memory, and domain data simultaneously.
+
+---
+
+## Two ways to use it
+
+PyCodeKG is designed to be useful at both ends — as a standalone command-line analysis tool, and as a structured context layer for AI agents.
+
+### 1. Standalone — `pycodekg analyze`
+
+This single command is the actual reason I wrote this module. I got tired of my LLM doing grep on my src/ in order to get a good analysis of the codebase. This command runs fifteen analysis passes in seconds and the output drops straight into your favorite coding LLM for targeted improvement suggestions. I used this process to iteratively improve PyCodeKG and several of the analysis passes were added as a result.
+
+The analysis/ has files *_analysis_<date>.md - I ran PyCodeKG against **numpy** and **matplotlib** for fun.
+
+```bash
+pycodekg init                                        # downloads embedder
+pycodekg build --repo .                              # one-time index
+pycodekg analyze.                                    # the full report
+```
+
+**Note**
+The first-time run can take some time to warm up. Be patient.
+
+The 15-phase pipeline runs in sequence and surfaces several important metrics:
+
+| # | Phase | What it surfaces |
+|---|-------|-----------------|
+| 1 | Baseline metrics | Node/edge counts, graph shape |
+| 2 | CodeRank (global PageRank) | Structurally most important symbols |
+| 3 | Fan-in analysis | Heavily depended-on functions (breaking-change risk) |
+| 4 | Fan-out analysis | Orchestrators and complexity hotspots |
+| 5 | Dependency analysis | Orphaned / dead code candidates |
+| 6 | Pattern detection | Anti-patterns and structural red flags |
+| 7 | Module coupling | Tightly coupled pairs, import graph density |
+| 8 | Critical paths | Longest call chains, bottlenecks |
+| 9 | Public API identification | Exposed vs. internal surface |
+| 10 | Docstring coverage | By module, class, function, method |
+| 11 | Inheritance hierarchy | Depth, multiple inheritance, diamond patterns |
+| 12 | Insight synthesis | Issues + strengths callouts |
+| 13 | Snapshot history | Metric trends across releases |
+| 14 | Structural centrality (SIR) | Bridge nodes, graph removal impact |
+| 15 | Concern-based ranking | Nodes grouped by architectural concern |
+
+Every finding maps to a file and line number — no hallucinated signatures, no probabilistic guesses. The Markdown output is LLM-ready; the JSON snapshot is CI-gate-ready. Reach for `analyze` before any non-trivial refactor, at every release, and whenever you inherit an unfamiliar codebase. Full reference: [docs/Analyze.md](docs/Analyze.md).
+
+```bash
+pycodekg analyze --quiet --json ~/.claude/pycodekg_analysis_latest.json
+jq '.docstring_coverage.total' ~/.claude/pycodekg_analysis_latest.json
+```
+
+### 2. Agentic — MCP server for grounded AI workflows
+
+Run `pycodekg mcp` and Claude (or any MCP-aware client) gets nineteen tools backed by the same graph: `graph_stats`, `query_codebase`, `pack_snippets`, `get_node`, `list_nodes`, `callers`, `explain`, `centrality`, `bridge_centrality`, `framework_nodes`, `analyze_repo`, `snapshot_list / show / diff`, and more. Setup for Claude Code, Claude Desktop, Kilo Code, Copilot, and Cline is a single line — see [docs/MCP.md](docs/MCP.md) and [docs/INSTALLATION.md](docs/INSTALLATION.md).
+
+The agent benefit isn't subtle. Tools like `pack_snippets` return *actual source* with line numbers and surrounding context; `callers` returns the *real* fan-in resolved across import aliases, not a regex's best guess. The agent stops fabricating function signatures and starts citing them. Multi-step workflows — *"find the auth path, list its callers, summarize what changes if I rename it"* — collapse from dozens of `grep`s and file reads into a handful of source-grounded calls.
+
+Independent assessments tend to put it the same way:
+
+> "PyCodeKG compresses a multi-step workflow — semantic search, graph expansion, caller tracing, snippet retrieval, and architectural summarization — into a small set of tools that are fast to invoke and easy to chain. In practice, it let me move from broad orientation to intent-driven discovery and then to structural validation without dropping down into manual grep or repeated file reads."
+> — *GPT-5 (via Cline)*
+
+> "What sets it apart from 'search the repo with embeddings' tools is the structural layer… Verdict: 4.5/5 — recommend without reservation for any non-trivial Python codebase."
+> — *Claude Opus 4.7*
+
+> "PyCodeKG is dramatically more effective than traditional grep/file-reading workflows. Unique value: hybrid search combining natural-language intent with precise structural relationships."
+> — *Claude Haiku 4.5*
+
+Full reports in [assessments/](assessments/).
+
+---
+
+## Get started in 60 seconds
+
+**Requirements:** Python ≥ 3.12, < 3.14
+
+```bash
+pip install 'pycode-kg[viz,viz3d]'        # base + Streamlit + 3-D viewer
+
+cd /path/to/your/repo
+pycodekg init --repo .                    # download model, build graph, install hooks, snapshot
+pycodekg analyze .                        # the architectural report
+```
+
+That's the recommended path. Variants (minimal install, MCP-only, contributor setup) are in [docs/INSTALLATION.md](docs/INSTALLATION.md). Every CLI subcommand is also exposed as a script alias (`pycodekg-analyze`, `pycodekg-build`, `pycodekg-mcp`, …) for use in Makefiles and Poetry projects.
+
+---
+
+## How retrieval works
+
+Search is hybrid by design. A query like *"authentication flow"* runs in two phases:
+
+1. **Vector phase** — the query is embedded with a local sentence-transformer (cached after first download) and LanceDB returns the `k` closest functions, classes, and modules by cosine similarity.
+2. **Graph expansion phase** — each seed hit is expanded `hop` BFS steps along the typed edges (`CONTAINS`, `CALLS`, `IMPORTS`, `INHERITS`, `RESOLVES_TO`) so call chains and module relationships surface alongside the names that matched.
+
+**Structure is treated as ground truth; the embeddings are strictly an acceleration layer.** When the graph and the vector index disagree, the graph wins. This is why fan-in lookups are accurate even for same-named symbols across modules — `RESOLVES_TO` edges bridge call sites through their import aliases, and `callers()` does a two-phase reverse traversal that grep simply cannot replicate.
+
+The graph is built around four node kinds (module, class, function, method) and five edge relations. Schema and edge semantics are documented in [docs/CHEATSHEET.md](docs/CHEATSHEET.md).
+
+---
+
+## What you can do with it
+
+| If you want to… | Reach for | Detail |
+|---|---|---|
+| **Get a thorough architectural report** | `pycodekg analyze` | [docs/Analyze.md](docs/Analyze.md) |
+| **Generate a coherent architecture description** | `pycodekg architecture` | [docs/Architecture_usage.md](docs/Architecture_usage.md) |
+| **Track metrics across releases** | `pycodekg snapshot save / list / diff` | [docs/SNAPSHOTS.md](docs/SNAPSHOTS.md) |
+| **Identify the most structurally important code** | `pycodekg centrality` (SIR PageRank) | [docs/CODERANK.md](docs/CODERANK.md) |
+| **Pull source-grounded context for an LLM** | `pycodekg pack "..." --format md` | [docs/CHEATSHEET.md](docs/CHEATSHEET.md) |
+| **Run a hybrid semantic + structural query** | `pycodekg query "..."` | [docs/CHEATSHEET.md](docs/CHEATSHEET.md) |
+| **Browse the graph interactively** | `pycodekg viz` (Streamlit) | [docs/INSTALLATION.md](docs/INSTALLATION.md) |
+| **See call graphs in 3-D** *(active development — functional but rough)* | `pycodekg viz3d --layout funnel` | [docs/VIZ3D.md](docs/VIZ3D.md) |
+| **Wire it into Claude / Copilot / Cline** | `pycodekg mcp` | [docs/MCP.md](docs/MCP.md) |
+
+If you only read one doc after this one, read [docs/Analyze.md](docs/Analyze.md) — that's where most of the day-to-day value lives.
+
+---
+
+## Architecture
+
+```
+src/pycode_kg/
+├── visitor.py                       # AST extraction (three-pass: structure, calls, dataflow)
+├── graph.py                         # GraphBuilder: file discovery + dispatch
+├── store.py                         # SQLite persistence + canonical edges
+├── index.py                         # LanceDB semantic index
+├── pycodekg.py                      # Public façade
+├── pycodekg_query.py                # Hybrid query
+├── pycodekg_snippet_packer.py       # Source-grounded packs
+├── pycodekg_thorough_analysis.py    # `analyze` engine
+├── architecture.py                  # `architecture` description generator
+├── ranking/                         # PageRank, bridge centrality, framework nodes
+├── snapshots.py                     # Temporal metric snapshots
+├── analysis/                        # Coupling, cycles, orphans, hotspots
+├── cli/                             # All `pycodekg-*` entry points
+├── mcp_server.py                    # MCP server (nineteen tools)
+├── app.py                           # Streamlit web app
+├── viz3d.py / layout3d.py           # PyVista/PyQt5 3-D viewer
+└── viz3d_timeline.py                # Metric history timeline
+```
+
+The MCP server, the CLI, and the Streamlit app are thin wrappers over the same store + index + ranking core — there is exactly one code path for each capability. The latest architectural deep-dive is in [docs/analysis_v0.19.0.md](docs/analysis_v0.19.0.md), produced (of course) by `pycodekg analyze` against this very repo.
+
+---
+
+## Documentation map
+
+| Doc | What it covers |
+|---|---|
+| [docs/INSTALLATION.md](docs/INSTALLATION.md) | All install variants, MCP setup, contributor setup, troubleshooting |
+| [docs/Analyze.md](docs/Analyze.md) | The `analyze` command — every metric, every flag, interpretation guide |
+| [docs/Architecture_usage.md](docs/Architecture_usage.md) | Generating coherent architecture descriptions |
+| [docs/SNAPSHOTS.md](docs/SNAPSHOTS.md) | Temporal metric snapshots, diffing across releases |
+| [docs/CODERANK.md](docs/CODERANK.md) | SIR PageRank, bridge centrality, framework hubs |
+| [docs/MCP.md](docs/MCP.md) | MCP server setup for Claude / Kilo / Copilot / Cline, tool reference |
+| [docs/CHEATSHEET.md](docs/CHEATSHEET.md) | Every CLI flag and every MCP tool — one page |
+| [docs/VIZ3D.md](docs/VIZ3D.md) | The 3-D PyVista viewer and layouts |
+| [CHANGELOG.md](CHANGELOG.md) | Release history |
+
+---
+
+## Citation
+
+If you use PyCodeKG in your research or project, please cite it:
+
+[![DOI](https://zenodo.org/badge/1202379010.svg)](https://zenodo.org/badge/latestdoi/1202379010)
+
+> Suchanek, E. G. (2026). *PyCodeKG: A Knowledge Graph for Python Codebases* (Version 0.19.0) [Software]. Flux-Frontiers. https://doi.org/10.5281/zenodo.19834777
+
+```bibtex
+@software{suchanek_pycode_kg,
+  author    = {Suchanek, Eric G.},
+  title     = {{PyCodeKG}: A Knowledge Graph for Python Codebases},
+  version   = {0.19.0},
+  year      = {2026},
+  publisher = {Flux-Frontiers},
+  url       = {https://github.com/Flux-Frontiers/pycode_kg},
+  doi       = {10.5281/zenodo.19834777},
+}
+```
+
+---
+
+## License
+
+[Elastic License 2.0](https://www.elastic.co/licensing/elastic-license) — free for non-commercial and internal use; commercial redistribution or hosting requires a license from Flux-Frontiers.
+
+---
+
+## Support & acknowledgments
+
+- **Issues** — [GitHub Issues](https://github.com/Flux-Frontiers/pycode_kg/issues)
+- Sister projects [DocKG](https://github.com/Flux-Frontiers/doc_kg) and [MetaboKG](https://github.com/Flux-Frontiers/metabo_kg)
+- LanceDB, sentence-transformers, PyVista, Streamlit, and FastMCP for the foundations
+
+---
+
+*Built for Python developers and AI agents that work alongside them — egs · Last updated May 2026*

{pycode_kg-0.18.2 → pycode_kg-0.19.1}/pyproject.toml

@@ -66,7 +66,7 @@ ruff = ">=0.4.0"
 # ---------------------------------------------------------------------------
 [project]
 name = "pycode-kg"
-version = "0.18.2"
+version = "0.19.1"
 description = "A tool to build a searchable knowledge graph from Python repositories"
 readme = "README.md"
 license = "Elastic-2.0"
@@ -94,7 +94,7 @@ dependencies = [
     "safetensors>=0.5.0",
     "sentence-transformers>=5.4.1",
     "torch>=2.5.1",
-    "transformers>=4.57.6",
+    "transformers>=4.40.0,<4.57",
     "kgmodule-utils>=0.2.1",
 ]
 

{pycode_kg-0.18.2 → pycode_kg-0.19.1}/src/pycode_kg/__init__.py

@@ -32,7 +32,7 @@ KGModule SDK (build new domain KGs)::
     from pycode_kg import KGModule, KGExtractor, PyCodeKGExtractor, NodeSpec, EdgeSpec
 """
 
-__version__ = "0.18.2"
+__version__ = "0.19.1"
 __author__ = "Eric G. Suchanek, PhD"
 
 # Low-level primitives (locked v0 contract)